#22, document: update manual

nmfs-fish-tools · Nov 1, 2021 · d1d83fd · d1d83fd
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diff --git a/docs/manual/404.html b/docs/manual/404.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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diff --git a/docs/manual/SSMSE.html b/docs/manual/SSMSE.html
diff --git a/docs/manual/advanced-options-use-a-custom-management-strategyprocedure.html b/docs/manual/advanced-options-use-a-custom-management-strategyprocedure.html
diff --git a/docs/manual/glossary-of-mse-terms.html b/docs/manual/glossary-of-mse-terms.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
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diff --git a/docs/manual/helper.html b/docs/manual/helper.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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diff --git a/docs/manual/index.html b/docs/manual/index.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -226,7 +226,7 @@ <h1>
 <div id="header">
 <h1 class="title">SSMSE user manual</h1>
 <p class="author"><em>Kathryn Doering and Nathan Vaughan</em></p>
-<p class="date"><em>2021-10-20</em></p>
+<p class="date"><em>2021-11-01</em></p>
 </div>
 <div id="preface" class="section level1 unnumbered">
 <h1>Preface</h1>
@@ -245,12 +245,16 @@ <h2>R session information</h2>
 Matrix products: default
 
 locale:
-[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
-[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
+[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
+[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
+[5] LC_TIME=English_United States.1252    
 
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
+other attached packages:
+[1] SSMSE_0.2.2    testthat_3.0.4
+
 loaded via a namespace (and not attached):
 [1] r4ss_1.43.0  ss3sim_1.1.6</code></pre>
 

diff --git a/docs/manual/intro.html b/docs/manual/intro.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -356,13 +356,13 @@ <h2><span class="header-section-number">1.3</span> Brief description of the SSMS
 <li>The OM is created with create_OM()</li>
 <li>run_OM() runs the OM and creates the dataset to pass to the management strategy</li>
 <li>Parse_MS() is called, and runs the Management Strategy function (e.g., EM()), which projects catch forward.</li>
+<li>Update_OM() is called, which puts catch into the operating model.</li>
+<li>run_OM() runs the OM and creates the dataset to pass to the management strategy</li>
+<li>Parse_MS() is called, and runs the Management Strategy function (e.g., EM()), which projects catch forward.</li>
 <li>Determine if more years need to be projected. If yes, continue; if no, end simulation.</li>
-<li>Repeat steps 3-6.</li>
+<li>Repeat steps 5-8.
+<img src="images/ssmse_fxn_map.png" alt="The steps implemented in run_SSMSE() showing the functions called." /></li>
 </ol>
-<div class="figure">
-<img src="images/ssmse_fxn_map.png" alt="" />
-<p class="caption">The steps implemented in run_SSMSE() showing the functions called.</p>
-</div>
 <div id="conditioning-the-om-and-sampling-from-the-om" class="section level3" number="1.3.1">
 <h3><span class="header-section-number">1.3.1</span> Conditioning the OM and sampling from the OM</h3>
 <p>For each scenario, SSMSE starts with the user providing a fitted SSS3 model (or selecting an model from the SSMSE package) to use as an OM. For each iteration of the scenario, SSMSE turns the SS fitted model into an OM and runs it once with no estimation with Stock Synthesis in order to get the “true” values and a bootstrapped data set from SS3. Note that any modifications to the OM’s parameters specified by the users as it is extended forward in time are also applied.</p>
@@ -377,7 +377,7 @@ <h3><span class="header-section-number">1.3.3</span> Feedback from managment str
 </div>
 <div id="subsequent-runs-of-the-management-strategy" class="section level3" number="1.3.4">
 <h3><span class="header-section-number">1.3.4</span> Subsequent runs of the management strategy</h3>
-<p>The appended data set is then used in the managment strategy again, and new catch by fleet is produced that can then be fed back to the OM.</p>
+<p>The appended data set is then used in the management strategy again, and new catch by fleet is produced that can then be fed back to the OM.</p>
 
 </div>
 </div>

diff --git a/docs/manual/output.html b/docs/manual/output.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
-<meta name="date" content="2021-10-20" />
+<meta name="date" content="2021-11-01" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -228,9 +228,9 @@ <h1><span class="header-section-number">6</span> Output and Plots</h1>
 <div id="summarizing-output" class="section level2" number="6.1">
 <h2><span class="header-section-number">6.1</span> Summarizing output</h2>
 <p>Output is summarized using <code>SSMSE_summary_all()</code>:</p>
-<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb61-1"><a href="output.html#cb61-1" aria-hidden="true" tabindex="-1"></a>summary_list <span class="ot">&lt;-</span> <span class="fu">SSMSE_summary_all</span>(<span class="at">dir =</span> <span class="st">&quot;path/to/scenario/dir&quot;</span>,</span>
-<span id="cb61-2"><a href="output.html#cb61-2" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scenarios =</span> <span class="fu">c</span>(<span class="st">&quot;sample_low&quot;</span>, <span class="st">&quot;sample_high&quot;</span>),</span>
-<span id="cb61-3"><a href="output.html#cb61-3" aria-hidden="true" tabindex="-1"></a>                  <span class="at">run_parallel =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb65-1"><a href="output.html#cb65-1" aria-hidden="true" tabindex="-1"></a>summary_list <span class="ot">&lt;-</span> <span class="fu">SSMSE_summary_all</span>(<span class="at">dir =</span> <span class="st">&quot;path/to/scenario/dir&quot;</span>,</span>
+<span id="cb65-2"><a href="output.html#cb65-2" aria-hidden="true" tabindex="-1"></a>                  <span class="at">scenarios =</span> <span class="fu">c</span>(<span class="st">&quot;sample_low&quot;</span>, <span class="st">&quot;sample_high&quot;</span>),</span>
+<span id="cb65-3"><a href="output.html#cb65-3" aria-hidden="true" tabindex="-1"></a>                  <span class="at">run_parallel =</span> <span class="cn">TRUE</span>)</span></code></pre></div>
 <p>Relying on <code>ss3sim::get_results_all()</code>, this function creates:</p>
 <ul>
 <li>For each scenario, 3 scenario level .csv files</li>

diff --git a/docs/manual/plotting-output-and-performance-metrics.html b/docs/manual/plotting-output-and-performance-metrics.html
@@ -24,7 +24,7 @@
 <meta name="author" content="Kathryn Doering and Nathan Vaughan" />
 
 
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diff --git a/docs/manual/search_index.json b/docs/manual/search_index.json